> devtools::install_github("aertslab/SCopeLoomR", build_vignettes = TRUE)
Downloading GitHub repo aertslab/SCopeLoomR@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
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2: CRAN packages only
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4: data.table (1.13.6 -> 1.14.0 ) [CRAN]
5: XML (3.99-0.5 -> 3.99-0.6) [CRAN]
6: Rcpp (1.0.5 -> 1.0.6 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:3
Installing 1 packages: rlist
Installing package into ‘C:/Users/Nano/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.tuna.tsinghua.edu.cn/CRAN/bin/windows/contrib/4.0/rlist_0.4.6.1.zip'
Content type 'application/zip' length 236065 bytes (230 KB)
downloaded 230 KB
package ‘rlist’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Nano\AppData\Local\Temp\RtmpY1hSMf\downloaded_packages
√ checking for file 'C:\Users\Nano\AppData\Local\Temp\RtmpY1hSMf\remotes2b44266110a4\aertslab-SCopeLoomR-f065eae/DESCRIPTION' ...
- preparing 'SCopeLoomR':
√ checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'SCopeLoomR_0.11.0.tar.gz'
Installing package into ‘C:/Users/Nano/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'SCopeLoomR' ...
** using staged installation
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SCopeLoomR'
finding HTML links ... 好了
add_annotated_clustering html
add_annotation_by_cluster_annotation_mapping_df
add_clustering html
add_clustering_markers html
add_col_attr html
add_default_embedding html
add_embedding html
add_embedding_from_dyno html
add_fbgn html
add_global_attr html
add_global_md_annotation html
add_global_md_clustering html
add_global_md_clustering_kv html
add_global_md_embedding html
add_global_md_metric html
add_global_md_regulon_thresholds html
add_hierarchy html
add_matrix html
add_regulons html
add_regulons_AUC html
add_row_attr html
add_seurat_clustering html
append_clustering_update_ca html
build_loom html
check_global_meta_data html
check_missings html
chunk_points html
clear_global_meta_data html
close_loom html
col_attrs_exists_by_key html
compress_gzb64 html
convert_to_loom_v3_spec html
create_cluster_annotation html
create_hierarchy html
create_trajectory html
create_trajectory_from_dyno html
create_trajectory_from_monocle html
decompress_gzb64 html
finalize html
flush html
get_all_cluster_markers html
get_cell_annotation html
get_cell_ids html
get_cell_mask_by_cluster_name html
get_cluster_dgem_by_name html
get_cluster_info_by_cluster_name html
get_cluster_info_by_id html
get_cluster_markers html
get_cluster_names html
get_clustering_by_id html
get_clustering_idx_by_cluster_name html
get_clusterings html
get_clusterings_with_name html
get_col_attr_by_key html
get_default_embedding html
get_dgem html
get_dspace html
get_dtype html
finding level-2 HTML links ... done
Rd warning: C:/Users/Nano/AppData/Local/Temp/RtmpCUyHPZ/R.INSTALL36087ff170f5/SCopeLoomR/man/get_dtype.Rd:19: missing link 'hdf5r::h5types'
get_embedding_by_name html
get_embeddings html
get_genes html
get_global_attr html
get_global_md_clustering_by_id html
get_global_md_clustering_by_name html
get_global_md_clustering_info_by_name html
get_global_meta_data html
get_next_embedding_id html
get_regulon_thresholds html
get_regulons html
get_regulons_AUC html
get_row_attr_by_key html
get_seurat_clustering_resolutions html
global_meta_data_exists html
hdf5_utf8_encode html
hierarchy_exists html
init_global_md_embeddings html
init_global_meta_data html
is_base64_encoded html
is_gzipped html
is_json html
is_order_conserved html
list_clusterings_names html
lookup_all_global_attr html
lookup_loom html
open_loom html
remove_col_attr html
remove_global_attr html
remove_row_attr html
sce html
tSNE_expr html
update_cluster_descriptions_by_cluster_annotation_mapping_df
update_col_attr html
update_global_attr html
update_global_meta_data html
update_row_attr html
** building package indices
** installing vignettes
